Re: [AMBER] patching

From: Kenneth Huang <>
Date: Thu, 28 May 2015 14:55:09 -0400


There might be a way where you could specifically download individual
patches and then execute them, but someone else would probably be able to
give more information on how to do that.

That said, you just have to recompile, though I don't know why you wouldn't
want to patch the entire thing instead of just mmpbsa. I'd also suggest
using ambertools15, unless you have specific reasons not to.



On Thursday, May 28, 2015, George Tzotzos <> wrote:

> I’m using Amber12/AmberTools13
> Running throws on occasions the following error message.
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
> IOError: [Errno 2] No such file or directory:
> '_MMPBSA_complex_gb_surf.dat.0'
> Error occured on rank 0.
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> Running the same calculation on a different machine proceeds without a
> problem. Looking at the archive, I believe the problem can be fixed by
> applying patches to mmpbsa. Do I need to recompile, re-install
> Amber/AmberTools or is there a way to apply patches only to mmpbsa?
> Thanks in advance for any advice
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Received on Thu May 28 2015 - 12:00:03 PDT
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